Unjustifiable assumptions of homology

http://www.bio.fsu.edu/James/Ornithological%20Monographs%202009.pdf

Unjustifiable assumptions of homology incorporated
into data matrices.—The most glaring example of
this problem is the coding of avian and theropod
manual, carpal, and tarsal characters as if they were homologous, despite the ambiguity of the data, and despite the assumption this coding entails that
the BMT [birds are maniraptor theropods] hypothesis is correct a priori. 

Because of the above ambiguities, these five
sets of characters [the palate, the basipterygoid process, the carpus, the manus, and the tarsus] cannot be coded for birds and theropods without unjustified assumptions of
homology. They were not included in the primary
analysis of our matrix. This decision is
understood to be especially controversial, so
we have documented our reasoning, which was
based on careful review of the anatomical evidence,
in Appendix 3.

Criticisms of the James and Pourtless study:
http://theropoddatabase.blogspot.ca/2015/01/bandit-cladogram-evaluated-james-and.html

http://dml.cmnh.org/2009Apr/msg00230.html

http://dml.cmnh.org/2009Apr/msg00236.html

http://scienceblogs.com/tetrapodzoology/2009/06/08/birds-come-first-hypothesis/#comment-12898

https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=15&cad=rja&uact=8&ved=0CC4QFjAEOApqFQoTCPHX39mS-MgCFUxWHgod3RMGig&url=http%3A%2F%2Fwww4.ncsu.edu%2F~mhschwei%2FResearch_files%2FMakovicky___Zanno_2011_theropod_diversity_and_avian_characteristics-1.pdf&usg=AFQjCNFFUYs0N4rfq2F8aGPuSQSnEumwdw&sig2=cKMU3Gu8JjB9YDNvGjDDFQ&bvm=bv.106674449,d.cWw

James and Pourtless excluded the characteristics that are in dispute. That is impartial.
The critics object to that. The critics want things scored their way.

From pterosaur to primitive bird

Here is a draft of the lineage from pterosaur to primitive bird (click to enlarge):

This shows the transition from pterosaur to flying primitive birds and it also shows how the alvarezsaurids and oviraptors fit in as secondarily flightless primitive birds.

Connection of Rhamphorhynchoid pterosaurs to primitive birds:
http://pterosaurnet.blogspot.ca/2015/10/ancestor.html

Oviraptors as secondarily flightless primitive birds:
http://pterosaurnet.blogspot.ca/2014/09/oviraptors-as-secondarily-flightless.html

Connection of Jeholornis and Oviraptors:
http://pterosaurnet.blogspot.ca/2015/10/jeholornis-and-oviraptors.html

If anyone has a comment or a question, please feel free to submit it.

Jeholornis and Oviraptors

I suggest that secondarily flightless oviraptors descended (in both senses) from a flying creature like Jeholornis. Notice the similarities in morphology, time and location.

https://en.wikipedia.org/wiki/Jeholornis

Jeholornis (meaning "Jehol bird") is a genus of avialans that lived between approximately 122 and 120 million years ago during the early Cretaceous Period in China. Fossil Jeholornis were first discovered in the Jiufotang Formation in Hebei Province, China (in what was previously Rehe Province, also known as Jehol—hence the name) and additional specimens have been found in the older Yixian Formation.[1] Jeholornis had long tails and few small teeth, and were approximately the size of turkeys,[2] making them among the largest avialans known until the Late Cretaceous. Their diet included seeds of cycads, Ginkgo or similar plants. Jeholornis were relatively large, primitive avialans, with a maximum adult length of up to 80 cm (2.6 ft).[2] Their skulls were short and high, similar to other primitive avialans like Epidexipteryx and to early oviraptorosaurs like Incisivosaurus.

https://en.wikipedia.org/wiki/Avialae

Avialae is also occasionally defined as an apomorphy-based clade (that is, one based on physical characteristics). Jacques Gauthier, who named Avialae in 1986, re-defined it in 2001 as all dinosaurs that possessed feathered wings used in flapping flight, and the birds that descended from them.[8][9]

https://en.wikipedia.org/wiki/Oviraptorosauria

Oviraptorosaurs ("egg thief lizards") are a group of feathered maniraptoran dinosaurs from the Cretaceous Period of what are now Asia and North America. They are distinct for their characteristically short, beaked, parrot-like skulls, with or without bony crests atop the head. They ranged in size from Caudipteryx, which was the size of a turkey, to the 8 metre long, 1.4 ton Gigantoraptor.[4] The group (along with all maniraptoran dinosaurs) is close to the ancestry of birds. Analyses like those of Maryanska et al (2002) and Osmólska et al. (2004) suggest that they may represent primitive flightless birds.[5][6]

https://en.wikipedia.org/wiki/Caudipteridae

Caudipteridae is a family of oviraptorosaurian dinosaurs known from the Early Cretaceous of China. Found in the Yixian and Jiufotang Formations, the group existed between 125-120 million years ago.

https://en.wikipedia.org/wiki/Protarchaeopteryx

Protarchaeopteryx (meaning "before Archaeopteryx") is a genus of turkey-sized feathered theropod dinosaur from China.[1] Known from the Jianshangou bed of the Yixian Formation, it lived during the early Aptian age of the Early Cretaceous, approximately 124.6 million years ago.[2]

JEHOLORNIS



OVIRAPTOR

NOTE:
"Maniraptors" were either secondarily flightless avialae or secondarily flightless non-avialae paraves.
In either case, they descended from flying ancestors. They are not transitional between dinosaurs and Paraves.

Outgroups

There are many problems with the analyses of the dino to bird theory. Here is one of them:

http://www.bio.fsu.edu/James/Ornithological%20Monographs%202009.pdf

Also, the use of bipedal coelurosaurian
outgroups, as in the analysis by Clark et
al. (2002), may be contributing to a potentially
misleading topology. Outgroup choice determines
the polarity of character states, including
ancestral reconstructions for entire clades (Nixon
and Carpenter 1993). In this case, using bipedal
cursors as outgroups may obscure phylogenetic
signal by wrongly treating characters indicating
flight loss as plesiomorphy.

The "maniraptors" such as oviraptors and alvarezsaurids were flightless. They lived on the ground. The question is whether their ancestor was a ground-living creature (such as a dinosaur) or whether their ancestor was a flying, primitive bird.
When a cladistic analysis uses a ground-based dinosaur (eg. allosaurus) as the outgroup it takes the flightlessness of the "maniraptors" as being inherited from a dinosaur lineage, when in fact they actually descended (in both senses) from a flying primitive bird ancestor.

Ancestor

The ancestor of primitive birds was a rhamphorhynchoid pterosaur much like Jeholopterus or Pterorhynchus.
The earliest primitive birds were the feathered, flying creatures with long-bony-tails, such as the scansoriopterygids.

http://en.wikipedia.org/wiki/Scansoriopterygidae

The scansoriopterygids would have lived alongside synapsids such as the aquatic Castorocauda and arboreal gliding mammal Volaticotherium, the rhamphorhynchoid pterosaurs Jeholopterus and Pterorhynchus, as well as a diverse range of insect life (including mayflies and beetles) and several species of salamander.[14][15]

 http://www.ivpp.ac.cn/qt/papers/201206/P020120604508520389814.pdf

The [Epidendrosaurus] material described in this paper was collected from a new locality, Daohugou, in east Nei Mongol, northeast China, which is west of Liaoning Province. Many salamanders(Wang 2000), plants and insects (Zhang 2002)have recently been discovered from this new locality. It is notable that an anurognathid rhamphorhynchoid pterosaur [Jeholopterus] with beautiful hair [pycnofibers] covering the whole body has also been reported from this locality (Wang et al. 2002). The estimated age of the deposit at this locality is very controversial and ranges from the Middle Jurassic or the Early Cretaceous according to various authors (Wang etal. 2000; Zhang 2002); however, most workers currently regard it as being Late Jurassic.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842671/

Two other Chinese specimens were reported with integumental covering, coming from the same stratum (the Daohugou Bed) as Jeholopterus. So far we have not had the opportunity to examine this material. The first one is a small unnamed anurognathid with extensive preservation of soft tissue, including fibres that have been interpreted as protofeathers (Ji & Yuan 2002). The published pictures show that the soft tissue interpreted as protofeathers is of the same nature as the pycnofibres of Jeholopterus. 

 http://en.wikipedia.org/wiki/Pterosaur

At least some pterosaurs had hair-like filaments known as pycnofibres on the head and body, similar to, but not homologous (sharing a common structure) with, mammalian hair. Though a fuzzy "integument" (natural covering/outer coat) "was first reported in 1831" by Goldfuss,^[29] recent pterosaur finds and the technology for histological and ultraviolet examination of pterosaur specimens have provided incontrovertible proof: pterosaurs had pycnofibre coats. Pycnofibres were not true hair as seen in mammals, but a unique structure that developed a similar appearance. Although, in some cases, actinofibrils (internal structural fibres) in the wing membrane have been mistaken for pycnofibres or true hair, some fossils such as those of Sordes pilosus (which translates as "hairy demon") and Jeholopterus ninchengensis do show the unmistakable imprints of pycnofibres on the head and body, not unlike modern-day bats, another example of convergent evolution.^[21] The head-coats do not cover the pterosaur's large jaws in many of the specimens found so far.^[29]

https://en.wikipedia.org/wiki/Jeholopterus

Jeholopterus was a small anurognathid pterosaur from the Middle to Late Jurassic^[1] Daohugou Beds of the Tiaojishan Formation of Inner Mongolia, China , preserved with hair-like pycnofibres and skin remains.

http://link.springer.com/article/10.1360/02tb9054#page-1

We report a new and nearly completely articulated rhamphorhynchoid pterosaur, Jeholopterus ningchengensis gen. et sp. nov., with excellently preserved fibres in the wing membrane and “hairs” [pycnofibers] in the neck, body and tail regions. Many of its characteristics such as a short neck, short metacarpals and distinctively long fifth pedal digit are characteristic of rhamphorhynchoids. The new species can be further referred to the ‘strange’ short-tailed rhamphorhynchoid family Anurognathidae. It is much more complete than the other known members of the family, namely, Anurognathus from Solnhofen, Germany, Batrachognathus from Karatau, Kazakhstan, and Dendrorhynchoides from Beipiao, Liaoning Province, China. The new pterosaur also shows that the wing membrane is attached to the ankle of the hind limb. The pedal digits are webbed. Furthermore, the “hair” of Jeholopterus bears some resemblance to the hair-like integumental structures of the feathered dinosaur Sinosauropteryx although there is yet no direct evidence to argue for or against their homology.

http://dinosaur-museum.org/featheredinosaurs/rhamphorhynchoid.pdf

A new rhamphorhynchoid [Pterorhynchus] is described with a headcrest that is unprecedented among the long-tailed pterosaurs. The preservation of the headcrest presents significant implications regarding the physical appearance and aerodynamics of all pterosaurs. Also, "hair-like" integumentary structures of this pterosaur are shown to be complex multi-strand structures which presents evidence on the origin of feathers and the possibility of a remarkably early ancestral relationship between pterosaurs and birds.

https://en.wikipedia.org/wiki/Pterorhynchus

Pterorhynchus was a genus of rhamphorhynchid "rhamphorhynchoid" pterosaur from the Middle or Late Jurassic-age Daohugou Formation[1] of Inner Mongolia,China.

This type specimen consists of an articulated, nearly complete skeleton with remains of the integument. These included the wing membrane, hair-like structures, a long version of the vane found at the end of "rhamphorhynchoid" tails, and a head crest with both a low bony base and a large keratin extension; the latter feature is unusual in "rhamphorhynchoids" (i.e. basal pterosaurs), the fossils of which do not often show head crests.

The hairs (pycnofibers) were originally described as pinnate, with many strands arising from a single base (calamus), and seen as corresponding to the hypothetical Stage II in the evolution of feathers.

http://en.wikipedia.org/wiki/Yi_%28dinosaur%29

The only known Yi qi fossil was found in rocks assigned to the Tiaojishan Formation, dating to the Callovian-Oxfordian age of the Middle-Late Jurassic,[1] dated to between 165 and 153 million years ago.[3] This is the same formation (and around the same age) as the other known scansoriopterygids Epidexipteryx and Scansoriopteryx.

https://en.wikipedia.org/wiki/Darwinopterus

Darwinopterus (meaning "Darwin's wing") is a genus of pterosaur, discovered in China and named after biologist Charles Darwin. Between 30 and 40 fossil specimens have been identified,[1] all collected from the Tiaojishan Formation, which dates to the middle Jurassic period, 161-160.5 Ma ago.[2] The type species, D. modularis, was described in February 2010.[3] D. modularis was the first known pterosaur to display features of both long-tailed ('rhamphorhynchoid') and short-tailed (pterodactyloid) pterosaurs, and was described as a transitional fossil between the two groups.[4] Two additional species, D. linglongtaensis and D. robustodens, were described from the same fossil beds in December 2010 and June 2011, respectively.[5][6]

Darwinopterus, like its closest relatives, is characterized by its unique combination of basal and derived pterosaurian features. While it had a long tail and other features characteristic of the 'rhamphorhynchoids', it also had distinct pterodactyloid features, such as long vertebrae in the neck and a single skull opening in front of the eyes, the
nasoantorbital fenestra (in most 'rhamphorhynchoids', the antorbital fenestra and the nasal opening are separate).[5]

http://digitallibrary.amnh.org/handle/2246/6352
Turner et al 2012.

For reference:

https://en.wikipedia.org/wiki/Rhamphorhynchoidea

The Rhamphorhynchoidea forms one of the two suborders of pterosaurs and represent an evolutionary grade of primitive members of this group of flying reptiles. This suborder is paraphyletic in relation to the Pterodactyloidea, which arose from within the Rhamphorhynchoidea, not from a more distant common ancestor.

Suborder: Rhamphorhynchoidea Plieninger, 1901
Included groups
Anurognathidae Campylognathoididae Dimorphodontidae Eopterosauria Rhamphorhynchidae

JEHOLOPTERUS



PTERORHYNCHUS

SCANSORIOPTERYGIDAE

Primitive Birds

Here is a partial list of primitive (feathered, long-bony-tailed) flying and secondarily flightless birds.

Scansoriopterygids (Temporal range: Late Jurassic, 165–156 Ma)
Anchiornis (Temporal range: Late Jurassic, 161–160.5 Ma)
Aurornis (Temporal range: Late Jurassic, 160 Ma)
Xiaotingia (Temporal range: Late Jurassic, 160 Ma)
Zhongornis (Temporal range: Early Cretaceous, 122 Ma)
Oviraptors (secondarily flightless)

Zhenyuanlong?
Archaeopteryx?
Microraptor?
Eosinopteryx? (Temporal range: Late Jurassic, 160 Ma)
Pedopenna? (Temporal range: Middle or Late Jurassic, 164 Ma)
Jeholornis?
Alvarezsaurids?
Ornithomimosaurs?
Velociraptor?
Jixiangornis?

The flying primitive (feathered, long-bony-tailed) birds evolved from pterosaurs.
The secondarily flightless primitive birds evolved from the flying primitive birds. 

Basalmost Paraves

There is a set of 4-winged, flying, primitive birds (eg. Anchiornis, Aurornis, Xiaotingia etc.) that at times have been classified as avialans and sometimes as dromaeosaurids. They actually belong to the basalmost Paraves. 
They are the Tetrapterygidae and the Scansoriopterygids.

I suggest that these flying primitive birds evolved from pterosaurs.
Later, some of these primitive birds settled on the ground and became secondarily flightless (eg. eudromaeosaurids, oviraptors etc).


https://en.wikipedia.org/wiki/Paraves

the work of Xu et al. (2003), (2005) and Hu et al. (2009) provide examples of basal and early paravians with four wings,[10][11][12] adapted to an arboreal lifestyle who would only lose their hindwings when some adapted to a life on the ground and when avialans evolved powered flight.[13] Newer research also indicates that gliding, flapping and parachuting was another ancestral trait of Paraves, while true powered flight only evolved once, in the lineage leading to modern birds.[14]

https://en.wikipedia.org/wiki/Tetrapterygidae

Tetrapterygidae (meaning "four-wings") is a group of four-winged dinosaurs proposed by Sankar Chatterjee in the second edition of his book The Rise of Birds: 225 Million Years of Evolution, where he included Microraptor, Xiaotingia, Aurornis, and Anchiornis.[1] The group was named after the characteristically long flight feathers on the legs of all included species, as well as the theory that the evolution of bird flight may have gone through a four-winged (or "tetrapteryx") stage, first proposed by naturalist William Beebe in 1915.[2] Chatterjee suggested that all dinosaurs with four wings formed a natural group exclusive of other paravians, and that this family was the sister taxon to the group Avialae, although most phylogenetic analyses have placed the animals of his Tetrapterygidae elsewhere in Paraves, such as Xiaotingia, Aurornis, and Anchiornis being placed in Avialae.[3]

Zhenyuanlong

Zhenyuanlong  is a secondarily flightless member of Paraves.

http://www.nature.com/srep/2015/150716/srep11775/full/srep11775.html (2015)

A large, short-armed, winged dromaeosaurid (Dinosauria: Theropoda) from the Early Cretaceous of China and its implications for feather evolution

Regardless of the precise phylogenetic relationships of dromaeosaurids, Zhenyuanlong provides the first glimpse of feather morphologies in a short-armed dromaeosaurid. Feathers are not preserved on the holotype of Tianyuraptor, and the shortness of the forearm in this taxon led to the suggestion that its arms lacked aerodynamic function15. Although the arms of Zhenyuanlong are short, they supported large and complex wings comprised of pennaceous coverts, primaries, and secondaries, some of which are asymmetric. Whether these wings served any type of aerodynamic function is a separate question that can only be answered with biomechanical analysis, but the wings of Zhenyuanlong are strikingly similar to those of Microraptor in general size, morphology, and composition, albeit they are supported by much smaller arms.

The integumentary similarities between Zhenyuanlong and Microraptor-type animals could suggest one of several explanations. First, the large short-armed dromaeosaurids may have had some volant abilities, unrecognized previously because Tianyuraptor was preserved without feathers and its small arms were assumed to be un-flightworthy15. Perhaps there was not a large functional and behavioural gap between animals like Microraptor and Zhenyuanlong. We find this unlikely, however, given the striking differences in body size between them, and the incredibly short arms of Zhenyuanlong which do not appear optimized for flight (although we reiterate that biomechanical modelling is needed to properly test this). Alternatively, the integumentary similarities between small and clearly volant dromaeosaurids7 and larger and presumably non-volant dromaeosaurids could suggest that the larger and short-armed Zhenyuanlong evolved from more volant ancestors and maintained a many aspects of the integument through the inertia of common descent or for other selective reasons, not because it needed them for flight. It may be that such large wings comprised of multiple layers of feathers were useful for display purposes40, and possibly even evolved for this reason and not for flight, and this is one reason why they may have been retained in paravians that did not fly.

https://www.washingtonpost.com/news/speaking-of-science/wp/2015/07/16/scientists-find-a-new-dinosaur-with-well-preserved-bird-like-wings-but-not-for-flight/

Zhenyuanlong suni didn't have wings well suited for flight -- but it did have the feathers one would need to get off the ground. Because of this, they suspect that suni came after a flying ancestor, losing the capability for muscle-powered flight but retaining the related plumage, perhaps to use its wings for mating displays.

Primitive birds flying

Primitive birds (basalmost paraves) flapped their wings and flew using the same set of muscles as their pterosaur ancestors.

http://press.princeton.edu/witton/sa...pterosaurs.pdf At one stage, it was thought that the flight muscles of pterosaurs were very [modern] birdlike, with the arm lifted by a muscle, m. supracoracoideus, anchoring on the sternum rather than the shoulders. In birds, this muscle arcs over the glenoid to attach on the dorsal surface of the humerus, elevating the wing with a pulley-like system (e.g., Kripp 1943; Padian 1983a; Wellnhofer 1991a). Detailed reconstruction of the proximal arm musculature of pterosaurs shows that this is not the case, however, and that the [pterosaur] arm was more likely lifted by large muscles anchored on the scapula and back, and lowered by those attached to the sternum and coracoid (fig. 5.8; Bennett 2003a). Unlike [modern] birds, where two vastly expanded muscles are mainly used to power flight, it appears that pterosaurs used several muscle groups to form their flapping strokes.

https://repository.si.edu/bitstream/...=1&isAllowed=y

Furthermore, the supracoracoideus muscle, and hence an ossified sternum, is not necessary to effect the recovery stroke of the wing. Thus the main evidence for Archaeopteryx having been a terrestrial, cursorial predator is invalidated. There is nothing in the structure of the pectoral girdle of Archaeopteryx that would preclude its having been a powered flier.

Concerning the lack of asymmetric feathers in flying basalmost paraves, the following seems relevant: https://gwawinapterus.wordpress.com/...-introduction/ The basal deinonychosaur Anchiornis [a primitive bird] might offer a possible explanation. It had symmetrical feathers, but they were arranged in an unique away; in species with asymmetrical feathers, the most distally attached wing feathers are the longest ones. In Anchiornis, the longest are anchored near the wrist, making the center of the wing the broadest area. This is not an unusual profile among flightless maniraptors – oviraptors like Caudipteryx have this sort of arrangement as well. Anchiornis, however, differs in that the feathers at the front (as in, anchored more distally) of the longest feather decrease rapidly in size as they are closer to the end of the supporting digit; this results in a rounded, yet slightly pointy wing shape. It is possible that this arrangement could had been an early adaptation to the demands of powered flight, before true asymmetrical feathers evolved. If so, it is possible that Anchiornis did engage in powered flight, or even a method of escape akin to rudimentary WAIR. So far, no tests have been conducted to examine the aerodynamic capacities of it’s wings. In Anchiornis, the entire wing forms the airfoil. http://www.sciencedirect.com/science/article/pii/S0960982212011943 Primitive bird: In modern birds (Neornithes), the wing is composed of a layer of long, asymmetrical flight feathers overlain by short covert feathers [1-3]. It has generally been assumed that wing feathers in the Jurassic bird Archaeopteryx [4-9] and Cretaceous feathered dinosaurs [10, 11] had the same arrangement. Here, we redescribe the wings of the archaic bird Archaeopteryx lithographica [3-5] and the dinosaur Anchiornis huxleyi [12, 13] and show that their wings differ from those of Neornithes in being composed of multiple layers of feathers. In Archaeopteryx, primaries are overlapped by long dorsal and ventral coverts. Anchiornis has a similar configuration but is more primitive in having short, slender, symmetrical remiges. Archaeopteryx and Anchiornis therefore appear to represent early experiments in the evolution of the wing. This primitive configuration has important functional implications: although the slender feather shafts of Archaeopteryx [14] and Anchiornis [12] make individual feathers weak, layering of the wing feathers may have produced a strong airfoil. Furthermore, the layered arrangement may have prevented the feathers from forming a slotted tip or separating to reduce drag on the upstroke. The wings of early birds therefore may have lacked the range of functions seen in Neornithes, limiting their flight ability. Longrich NR, Vinther J, Meng Q, Li Q, Russell AP. https://en.wikipedia.org/wiki/Bird_flight Elliptical wings are short and rounded, having a low aspect ratio, allowing for tight maneuvering in confined spaces such as might be found in dense vegetation. As such they are common in forest raptors (such as Accipiter hawks), and many passerines, particularly non-migratory ones (migratory species have longer wings). They are also common in species that use a rapid take off to evade predators, such as pheasants and partridges.

Altogether we have a picture of a flying, feathered, 4 winged, arboreal, primitive bird with a long bony tail, that flew like a pterosaur. With elliptical wings and symmetric feathers

At times people have argued that a flying pterosaur would not devolve into a gliding primitive bird. But this is misguided, because the evidence indicates that flying pterosaurs evolved into flying primitive birds, not into gliding primitive birds.

Here are the aspects related to flight capability:

• muscles used 
• keeled or not keeled sternum 
• flight feathers (asymmetric or not) 
• feathered hindlimbs

See here for more details:
http://pterosaurnet.blogspot.ca/2010/05/keeled-breastbone.html
http://pterosaurnet.blogspot.ca/2015/07/primitive-birds-flying.html
http://pterosaurnet.blogspot.ca/2014/09/flight-without-supracoracoideus.html
http://pterosaurnet.blogspot.ca/2013/02/flight-stroke.html


http://www.nature.com/articles/ncomms14576 (2017)

A stiffer feathered postpatagium in Anchiornis may have compensated for its aerodynamically inferior arm feathers to some degree

Fingers - Quick Summary

 https://en.wikipedia.org/wiki/Origin_of_birds#Digit_homology

There is a debate between embryologists and paleontologists whether the hands of theropod dinosaurs and birds are essentially different, based on phalangeal counts, a count of the number of phalanges (fingers) in the hand. This is an important and fiercely debated area of research because its results may challenge the consensus that birds are descendants of dinosaurs.

Dinosaurs have hands with digits 2-3-4-x-x. (Roman numerals represent fingers, numbers represent phalanges).
But birds have hands with digits x-2-3-4-x.
This is a problem for the dino to bird theory.
To overcome this problem, the dino to bird folk propose changes that include the following:

• the loss of digit I 
• the reappearance of the lost digit IV
• digits II-III-IV adopting the phalangeal count and characteristics of the earlier digits I-II-III (via a frame shift) resulting in x-2-3-4-x with digit III the longest.  

The pterosaur transition (from 2-3-4-5-x) would be:

• the loss of digit I
• digits II-III-IV lose one phalange each, resulting in x-2-3-4-x with digit IV the longest (as in scansoriopterids). 

Note: The dino to bird folk do not consider scansoriopterids to be on the line leading to birds, but to have branched from that line.


Frame shift
http://www.researchgate.net/publication/259253962_Thumbs_down_a_molecular-morphogenetic_approach_to_avian_digit_homology

Thus the change of the phalangeal formula (as in the PRH) is actually caused by the change of the transcriptome (as in the FSH [frame shift hypothesis]), which in turn is directly caused by the loss of digit I (probably shh and hoxD mediated).

https://commons.wikimedia.org/wiki/File:Bird_and_dino_hand_difference_debate.JPG

Dinosaur to bird (notice the original loss of digit IV and its re-appearance)

In the diagram, Neotheropoda ( 1 ), basal tetanurae ( 2 ), a coelurosaurian ( 3 ), the bird (?)Archaeopteryx ( 4 ) and modern bird ( 5 ).

If scansoriopterygids are the basalmost members of paraves, then the very first paraves were (or were very similar to) the scansoriopterygids, which have x-2-3-4-x with digit IV being the longest.
Which is consistent with a pterosaur ancestry and contrary to a dino ancestry.

See here for more details:
http://pterosaurnet.blogspot.ca/2014/07/pterosaur-fingers.html

Bristles and feathers - Quick summary

Dinosaurs (eg. tyrannosaurs) had bristles. They did not have any form of feather.
On the other hand, pterosaurs had Stage I and Stage II feathers. Those early stage feathers kept the endothermic pterosaur warm, which was necessary in flying.
Primitive birds (basal paraves) had pennaceous feathers. Those pennaceous feathers developed in the transition from pterosaur to primitive bird.

In order to understand this topic, it is essential to understand the development stages a feather goes through.
Drawing B represents Stage I. Note that the follicle appears at Stage II (drawing C):

See here for more details:
http://pterosaurnet.blogspot.ca/2014/01/helpful-background.html

Primitive birds - Quick summary

There were pennaceous-feathered, long-bony-tailed primitive birds.
The most basal were flying (eg. scansoriopterygids, tetrapterygids).
Some later ones became secondarily flightless (eg. oviraptors, eudromaeosaurids etc).

These primitive birds have a great deal in common with pterosaurs. They evolved from pterosaurs.
These primitive birds have almost nothing in common with dinosaurs.

Scansoriopterygid

Oviraptor (secondarily flightless)

Oviraptor Propatagium

More evidence that oviraptors were secondarily flightless and not transitional between dinosaurs and Paraves.

https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=0CCMQFjAB&url=https%3A%2F%2Fbio.unc.edu%2Ffiles%2F2011%2F04%2FFeducciaCzerkas2015.pdf&ei=YEiHVfvbLMWRyAS67JKYBQ&usg=AFQjCNEJgIr2smR2Fi7zU35DviaiAu1sVg&sig2=R0xmD8EIWD2vnj8Zf__yMw&bvm=bv.96339352,d.aWw

Testing the neoflightless hypothesis: propatagium reveals flying ancestry of oviraptorosaurs (2015)
Alan Feduccia1• Stephen A. Czerkas2

Considerable debate surrounds the numerous
avian-like traits in core maniraptorans (oviraptorosaurs,
troodontids, and dromaeosaurs), especially in the
Chinese Early Cretaceous oviraptorosaur Caudipteryx,
which preserves modern avian pennaceous primary remiges
attached to the manus, as is the case in modern birds.
Was Caudipteryx derived from earth-bound theropod dinosaurs,
which is the predominant view among palaeontologists,
or was it secondarily flightless, with volant avians
or theropods as ancestors (the neoflightless hypothesis),
which is another popular, but minority view. The discovery
here of an aerodynamic propatagium in several specimens
provides new evidence that Caudipteryx (and hence oviraptorosaurs)
represent secondarily derived flightless
ground dwellers, whether of theropod or avian affinity, and
that their presence and radiation during the Cretaceous may
have been a factor in the apparent scarcity of many other
large flightless birds during that period.

There is actually no link between dinosaurs and Paraves.

See here for more details about oviraptors as secondarily flightless:
http://pterosaurnet.blogspot.ca/2014/09/oviraptors-as-secondarily-flightless.html

Dinosaurs are not similar to primitive birds

The following study shows that there were 51 synapomorphies (unique defining characteristics) for Paraves (primitive birds). This means that of the 374 characteristics that were evaluated, 51 of them were different than the claimed dinosaur ancestor. This is more than 1 in 8. This means that primitive birds are not similar to dinosaurs, which is a point that I have being making for a very long time. It is good to see a cladistic analysis confirm this point. 
Note that this number would be very much larger if the oviraptors etc were taken as secondarily flightless.

2011 study (Xu et al):
http://www.nature.com/nature/journal/v475/n7357/full/nature10288.html
http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf
 An Archaeopteryx-like theropod [Xiaotingia] from China and the origin of Avialae

Here we report a new Archaeopteryx-like theropod from China. This find further demonstrates that many features formerly regarded as being diagnostic of Avialae, including long and robust forelimbs, actually characterize the more inclusive group Paraves (composed of the avialans and the deinonychosaurs). 

Paraves: 1.1, 10.1, 13.0, 14.0, 15.1, 20.1, 21.1, 28.1, 39.0, 61.1, 65.0, 66.0, 69.0, 79.0, 91.0,95.0, 96.1, 97.1, 106.0, 109.1, 119.1, 125.0, 127.1, 129.1, 137.1, 138.1, 139.1, 154.0, 155.1,156.1, 160.1, 166.0, 176.1, 179.1, 180.1, 184.1, 202.1, 221.1, 232.0, 237.1, 262.1, 267.1,277.2, 292.0, 304.2, 306.1, 319.1, 320.2, 336.1, 354.0, and 362.1

Yi qi

Yi qi study:
https://www.researchgate.net/publication/275669107_A_bizarre_Jurassic_maniraptoran_theropod_with_preserved_evidence_of_membranous_wings

A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings 

The wings of birds and their closest theropod relatives share a uniform fundamental architecture, with pinnate flight feathers as the key component1, 2, 3. Here we report a new scansoriopterygid theropod, Yi qi gen. et sp. nov., based on a new specimen from the Middle–Upper Jurassic period Tiaojishan Formation of Hebei Province, China4. Yi is nested phylogenetically among winged theropods but has large stiff filamentous feathers of an unusual type on both the forelimb and hindlimb. However, the filamentous feathers of Yi resemble pinnate feathers in bearing morphologically diverse melanosomes5. Most surprisingly, Yi has a long rod-like bone extending from each wrist, and patches of membranous tissue preserved between the rod-like bones and the manual digits. Analogous features are unknown in any dinosaur but occur in various flying and gliding tetrapods6, 7, 8, 9, 10, suggesting the intriguing possibility that Yi had membranous aerodynamic surfaces totally different from the archetypal feathered wings of birds and their closest relatives. Documentation of the unique forelimbs of Yi greatly increases the morphological disparity known to exist among dinosaurs, and highlights the extraordinary breadth and richness of the evolutionary experimentation that took place close to the origin of birds.

Supplementary information:

If a membrane is reconstructed lateral to the trunk, the wing is similar in outline to ........ a pterosaur wing if the styliform element is approximately laterally oriented.

Extended data:
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14423.html#extended-data

Abstract:
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14423.html

Yi qi is the perfect candidate for transitional between pterosaur and paraves.

Here are a few other references:
http://phenomena.nationalgeographic.com/2015/04/29/chinese-dinosaur-had-bat-like-wings-and-feathers/

These wings were mutually exclusive: dinosaur or pterosaur, feathery or leathery. But Yi went for both options! It had membrane wings with a feathery covering on the leading edge. It shows that at least some dinosaurs had independently evolved the same kind of wings as pterosaurs—an extraordinary example of convergent evolution.

http://www.nature.com/articles/nature14392.epdf?referrer_access_token=ZfVGgFg7XRdurry3TN0QoNRgN0jAjWel9jnR3ZoTv0PiQtvFAER-nO6rVanRtj7cIVRMaXAe5x5JlY3vpNDkkxI0a1Q8_ZTmq63AsO-pCE_wZ6-LixrY3IBCK0O57ofs-sVhrdtkwoPKG1MmYYRWBnKtWySldMOVBfPZhs5YnU3psTTjZa6_HEcPzvjKZvRO962MU9ssjnM38C1xE3d-slSGO5xkY9Myf0Z8kfmYNxU%3D&tracking_referrer=www.nature.com

http://www.nature.com/news/more-on-unicorns-1.17419

It is here that we enter unicorn territory — for no dinosaur, however unusual, has been found with anything like this feature. The authors are appropriately cautious, therefore, in their interpretation.

http://www.theguardian.com/science/lost-worlds/2015/apr/29/bird-yi-qi-the-dinosaur-evolution-flight-feather-nature

https://whyevolutionistrue.wordpress.com/2015/04/30/dino-bat-a-new-flying-dinosaur-with-membranous-wings/

https://www.sciencenews.org/article/dinosaur%E2%80%99s-ride-may-have-been-glide

A dinosaur called Yi qi appears to have lifted a page from pterosaurs’ flight plan. Protruding from each of the newly discovered dinosaur’s wrists was a weird rodlike bone that may have attached to a fleshy wing that helped the dinosaur glide or fly, researchers report April 29 in Nature.“We’ve never seen anything like this in a dinosaur before,” says paleontologist Sarah Werning of Stony Brook University in New York. “It’s almost like this dinosaur was pretending to be a pterosaur.”

https://www.researchgate.net/publication/275669107_A_bizarre_Jurassic_maniraptoran_theropod_with_preserved_evidence_of_membranous_wings
Xu et al "identify the three manual digits of Yi and other maniraptors as II-III-IV".

https://images.nature.com/full/nature-assets/nature/journal/v521/n7550/extref/nature14423-s1.pdf

The Pterosaur Model (not shown) differs from the Bat Model in having
a laterally oriented styliform element (which is redundant functionally with the elongated manual digit IV), but otherwise is nearly identical to the Bat Model.

A key weakness of the Bat and Pterosaur Models is that no membranous soft tissue is preserved lateral to the body and posterior to the humerus and ulna in the holotype of Yi qi, whereas relatively large feathers are clearly present in this region. The feathers may simply have been situated ventrally and/or dorsally on the membrane, for purposes of insulation and/or display, but their large size implies that they might then have increased the drag experienced by the animal to strongly disadvantageous levels.

The major strength of the Bat and Pterosaur Models is that the reconstructed wing has a large membranous area and represents a general type of aerodynamic apparatus that is common among volant tetrapods other than birds and their close relatives 14-19,22

Kevin Padian commentary:

https://www.nature.com/articles/nature14392.epdf?referrer_access_token=_dLCCVvlPegFyP3c4GsuFtRgN0jAjWel9jnR3ZoTv0PiQtvFAER-nO6rVanRtj7cIVRMaXAe5x5JlY3vpNDkkxI0a1Q8_ZTmq63AsO-pCE_ObpObUo01kQljGZf1pg1VspxlgGl1ag1_Ppi_rb_KR7QdR4znn2erMDIpDZm-cbNYt9xObOVZ_5AGyUA2Z_P6ucWWcItD4wgO7HN6CfeNNw%3D%3D&tracking_referrer=www.nature.com



Note that David Peters make an interesting case for the idea that the Yi qi "styliform element" is a displaced radius and ulna.
https://pterosaurheresies.wordpress.com/2015/05/03/no-styliform-element-on-yi-qi-thats-just-a-displaced-radius/
https://pterosaurheresies.wordpress.com/2015/05/04/yi-qi-and-occams-razor/